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Food packaging plays a critical role in preserving the freshness and quality of foods while preventing microbial spoilage. Advances in this field have led to the development of intelligent and active packaging systems incorporating nanotechnology. Among these, electrospinning has gained attention for producing nanofibrous materials with high surface-to-volume ratios, enabling the efficient loading of active agents.In response to the growing concern over antibiotic-resistant bacteria, this study investigates the use of bacteriophages as an alternative antimicrobial agent. Lytic bacteriophages targeting Escherichia coli were isolated from Caspian seawater and immobilized onto electrospun nanofibers composed of polyvinyl alcohol (PVA), polycaprolactone (PCL), and bacterial nanocellulose (BNC). SEM confirmed successful phage immobilization, while TEM revealed their classification within the Siphoviridae and Podoviridae families.The addition of PCL to PVA enhanced the fibers' mechanical strength, reduced defects, and improved water resistance. Incorporating BNC further strengthened the nanofiber structure and enhanced its matrix properties. Antimicrobial testing using the disc diffusion method revealed an inhibition halo of 13 mm, exceeding that of the antibiotic ampicillin. Notably, the functionalized nanofibers retained antimicrobial efficacy for up to one month, with stable phage viability at 24°C, 4°C, and -20°C.These findings demonstrate the potential of electrospun nanofibers functionalized with bacteriophages as a sustainable solution for combating bacterial contamination in food packaging, contributing to enhanced food safety and extended shelf life.

In the present study, the effectiveness of a controlled-release drug delivery system of chitosan hydrogel loaded with ketorolac and buprenorphine on oxidative stress indices and albumin changes in the experimental bone defect model was considered.

After creating an experimental defect in the right tibia of each rat, 5 groups, including (A) the control group that did not receive any pharmacological intervention, (B) the chitosan hydrogel receiving group, (C) the group receiving chitosan hydrogel loaded with buprenorphine, (D) the group receiving chitosan hydrogel loaded with ketorolac, and (E) the group receiving chitosan hydrogel loaded with ketorolac and buprenorphine, were considered. Serum concentrations of antioxidant factors and albumin levels were then measured on days 0, 3, 7, and 21 after surgery.

In the control group, the maximum amount of oxidative stress and the maximum activity of antioxidant enzymes on the third and seventh days were compared between the 4 treatment groups. Moreover, the maximum amount of albumin on the third day was recorded and compared between the 4 other treatment groups. In 4 treatment groups, a significant decrease was observed in the mean of parameters related to oxidative stress compared to the control group, which was more noticeable in the group receiving ketorolac.

In the present study, the highest rate of control of oxidative stress conditions was observed in the group treated with the ketorolac-loaded chitosan hydrogel system, possibly due to its antioxidant properties and better control of inflammatory conditions caused by the use of chitosan and ketorolac in this treatment group.

The pathophysiological progression of traumatic spinal cord injury (SCI) includes primary and secondary injury. Secondary injury causes the destruction of the spinal cord tissue and neurological disorders. After primary mechanical damage, inflammation is the most important factor inducing astrogliosis and scar formation. The activation of inflammatory cells in the area of ​​damage causes the production of free radicals, all of which damage cell membranes. A significant level of oxygen free radical production is involved in the pathology of SCI; Therefore, limiting secondary damage is very important in the clinical treatment of acute traumatic spinal cord injury.

In this review article, the articles indexed in various databases were used. The collection of articles was evaluated without time constraints using keywords inducing traumatic spinal cord injury (SCI), inflammation, oxidative stress, chitosan, selenium nanoparticles.

Inflammation and oxygen free radicals play a key role in secondary damage after SCI. Therefore, as a new therapeutic approach, the use of - hydrogels based on chitosan has been considered in SCI. The biocompatibility and biological properties of chitosan have made it considered as a suitable material for nerve regeneration.

The use of reactive oxygen species scavengers, including metal nanoparticles, can control inflammation and oxidative stress in spinal cord injuries. Selenium nanoparticles treatment may reduce secondary damage in SCI by using its anti-inflammatory and antioxidant properties. Therefore, the use of selenium nanoparticles in the chitosan hydrogel bed can control the degeneration and functional improvement of the nerve tissue of the spinal cord.

In this study, a controlled release drug delivery system loaded with piroxicam and methadone was synthesized and used subcutaneously in rat with experimental tibial defect and healing were assessed histopathologically.

For this purpose 100 adult female rats were were randomly divided into five equal groups; group control, chitosan group, piroxicam group, methadone group, and piroxicam-methadone group. The morphological structure of the synthesized drug systems was studied by scanning electron microscope. In addition, the structure of the hydrogels was investigated by fourier transform infrared spectroscopy and while releasing the hydrogels gelation time, the release of piroxicam and methadone from the hydrogels were evaluated in vitro.  

 Histological results of the 3rd day of the study showed the lowest extent and severity of inflammation in the chitosan, piroxicam, and piroxicam-methadone groups, while on the 7th day, tissue inflammation and the extent of bleeding was lower in the piroxicam, methadone, and piroxicam-methadone groups than in the other groups. Evaluation of new bone formation on day 21 showed that the chitosan, piroxicam, and methadone groups had better repair than the other groups.

It seems that in the control group that did not receive any treatment intervention, following the experimental bone defect, the highest inflammatory response was observed in histological examination and finally the weakest bone repair. On the other hand, the presence of piroxicam, methadone and chitosan in the piroxicam-methadone group (all of which have anti-inflammatory effects) also seems to have a negative effect on repair.

Ras proteins are considered as one of the most critical cancer initiators. Mutations of this protein family lead to the continuous activation of the proliferation pathways. Therefore, many efforts have been taken to design the anti-mutant Ras drug candidates. Regardless of the development of promising inhibitors of Ras G12C mutant in a specific cancer type, there is no approved inhibitor of Ras mutants in the clinic. One of the significant limitations is to inhibit particular mutants and not to affect the wild-type Ras variants. Here we present a review on the mechanism of action of the Ras proteins to get a better insight into the strategies utilized to inhibit Ras-mutated cancers. The direct Ras inhibition strategies are then highlighted to obtain a better perspective of possible promising approaches to target Ras proteins in cancer therapy

Riboswitches are short regulatory elements generally found in the untranslated regions of prokaryotes’ mRNAs and classified into several families. Due to the binding possibility between riboswitches and antibiotics, their usage as engineered regulatory elements and also their evolutionary contribution, the need for bioinformatics tools of riboswitch detection is increasing. We have previously introduced an alignment independent algorithm for the identification of frequent sequential blocks in the families of riboswitches. Herein, we report the application of block location-based feature extraction strategy (BLBFE), which uses the locations of detected blocks on riboswitch sequences as features for classification of seed sequences. Besides, monoand dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods as some feature extraction strategies were investigated.

The classifiers of the Decision tree, KNN, LDA, and Naïve Bayes, as well as k-fold crossvalidation, were employed for all methods of feature extraction to compare their performances based on the criteria of accuracy, sensitivity, specificity, and f-score performance measures.

The outcome of the study showed that the BLBFE strategy classified the riboswitches indicating 87.65% average correct classification rate (CCR). Moreover, the performance of the proposed feature extraction method was confirmed with average values of 94.31%, 85.01%, 95.45% and 85.38% for accuracy, sensitivity, specificity, and f-score, respectively.

Our result approved the performance of the BLBFE strategy in the classification and discrimination of the riboswitch groups showing remarkable higher values of CCR, accuracy, sensitivity, specificity and f-score relative to previously studied feature extraction methods.

Gastric cancer (GC) is one of the leading causes of cancer mortality, worldwide. Molecular understanding of GC’s different subtypes is still dismal and it is necessary to develop new subtype-specific diagnostic and therapeutic approaches. Therefore developing comprehensive research in this area is demanding to have a deeper insight into molecular processes, underlying these subtypes. In this study, a three-step methodology was developed to identify important genes and subnetworks in two subtypes of GC (TP53+ and TP53-). First, weighted gene co-expression network analysis was performed to explore co-expressed gene modules in both subtypes. Afterward, the relationship of each module with the tumor pathological stage (as a clinical trait indicating tumor progression) was studied by decision tree machine learning algorithm and the best predicting module was selected for further analysis (modules with 241 genes for TP53+ and  1441 genes for TP53- were identified). Subsequently, a motif exploring and motif ranking analysis was implemented to explore three-member signature gene motifs in the selected modules' biological network. These motifs may have key regulatory roles in the studied GC subtypes. Motif members of TP53- mostly contain MAPK signaling pathway genes which show their key role in this subtype of GC. In the case of the TP53+ subtype, our findings demonstrated that alternative splicing and SNARE proteins could prompt the initiation and advancement of the disease. These findings can be used to develop new diagnostic and therapeutic approaches based on the personalized medicine concept. This methodology could be implemented to unravel underlying mechanisms and pathways in other complex phenotypes and diseases.

Riboswitches are special non-coding sequences usually located in mRNAs’ un-translated regions and regulate gene expression and consequently cellular function. Furthermore, their interaction with antibiotics has been recently implicated. This raises more interest in development of bioinformatics tools for riboswitch studies. Herein, we describe the development and employment of novel block location-based feature extraction (BLBFE) method for classification of riboswitches.

We have already developed and reported a sequential block finding (SBF) algorithm which, without operating alignment methods, identifies family specific sequential blocks for riboswitch families. Herein, we employed this algorithm for 7 riboswitch families including lysine, cobalamin, glycine, SAM-alpha, SAM-IV, cyclic-di-GMP-I and SAH. Then the study was extended toward implementation of BLBFE method for feature extraction. The outcome features were applied in various classifiers including linear discriminant analysis (LDA), probabilistic neural network (PNN), decision tree and k-nearest neighbors (KNN) classifiers for classification of the riboswitch families. The performance of the classifiers was investigated according to performance measures such as correct classification rate (CCR), accuracy, sensitivity, specificity and f-score.

As a result, average CCR for classification of riboswitches was 87.87%. Furthermore, application of BLBFE method in 4 classifiers displayed average accuracies of 93.98% to 96.1%, average sensitivities of 76.76% to 83.61%, average specificities of 96.53% to 97.69% and average f-scores of 74.9% to 81.91%.

Our results approved that the proposed method of feature extraction; i.e. BLBFE method; can be successfully used for classification and discrimination of the riboswitch families with high CCR, accuracy, sensitivity, specificity and f-score values.

Ketamine is a dissociative anesthetic that because of its minimal effects on respiratory and cardiovascular systems, frequently used in both human and veterinary medicine. But in recent years, it was recognized as a problematic drug of abuse and became increasing popular in many parts of the world. According to the United Nations Office on Drugs and Crime report, use of ketamine in East Asia, Australia, North America and Europe was increasing, also in parts of South East Asia because of less International Drug Control and availability of ketamine use of its dramatically increased. Recent studies showed that abuse and long-term use of ketamine cause changes in mood, and physical condition such as damage in the urinary tract, nervous tissue and liver failure among consumers. The review article is written by the keywords “ketamine, anesthesia, abuse”. articles that published in 1978- 2016 were selected. In this study, ketamine introduced initially; then use, abuse, damage caused by arbitrary use and legality of ketamine in some countries discussed and finally methods for the determination of ketamine were mentioned.

Some non-coding RNAs have an important role in the regulation of gene expression and consequently cellular function. Riboswitches are examples of these regulatory RNAs. Riboswitches are classified into various families according to sequential and structural similarities.
In this study, a block finder algorithm for identification of frequently appearing sequential blocks in five families of riboswitches from Rfam 12.0 database, without the use of alignment methods, was developed.
The developed program identified 21 frequently appearing blocks in five families of riboswitches.
Comparison of the results of the proposed algorithm with those of sequential alignment methods revealed that our method can recognize most of the patterns present in conserved areas of individual riboswitch families and determine them as specific blocks, implying potential of the developed program as a platform for further studies and developments.

Ascorbyl palmitate (AP) is an example of natural secondary food antioxidant, which has been used for oxidative rancidity prevention in food industry. In this study, the interaction of AP with bovine serum albumin (BSA) was investigated.
The mechanism of BSA interaction with AP was investigated using spectroscopic methods (UV-Vis, fluorescence). The thermodynamic parameters including enthalpy change (ΔH), entropy change (ΔS), and Gibb’s free energy (ΔG) were calculated using Van’t Hoff equation at different temperatures.
The experimental results showed that UV-Vis absorption spectra of BSA decreased upon increasing AP concentration, indicating that the AP can bind to BSA. Formation of the AP-BSA complex was approved by quenching of fluorescence and the quenching mechanism was found to be resultant from dynamic procedure. The positive values of both ΔH and ΔS showed that hydrophobic forces were the major binding forces. The negative value of ΔG demonstrated that AP interacts with BSA spontaneously. Molecular docking results confirmed that AP binds to BSA through hydrophobic forces.
The attained results showed that AP can bind to BSA and effectively distributed into the bloodstream.

The interactions between biomacromolecules such as serum albumin (SA) and various drugs have attracted increasing research attention in recent years. However, the study of SA with those drugs that have relatively high hydrophilicity and a lower affinity for SA could be a challenging issue. At the present study, the interaction of bovine SA (BSA) with neomycin as a hydrophilic drug has been investigated using surface plasmon resonance (SPR) and molecular docking methods.
BSA was immobilized on the carboxymethyl dextran hydrogel sensor chip after activation of carboxylic groups through NHS/EDC and, then, the neomycin interaction with BSA at different concentrations (1-128 µM) was investigated.
Dose-response sensorgrams of BSA upon increasing concentration of neomycin has been shown through SPR analysis. The small KD value (4.96 e-7 at 40°C) demonstrated high affinity of neomycin to BSA. Thermodynamic parameters were calculated through van’t Hoff equation at 4 different temperatures. The results showed that neomycin interacts with BSA via Van der Waals interactions and hydrogen bonds and increase of KD with temperature rising indicated that the binding process was entropy driven. Molecular docking study confirmed that hydrogen bond was the major intermolecular force stabilizing neomycin-BSA complex.
The attained results showed that neomycin molecules can efficiently distribute within the body after interaction with BSA in spite of having hydrophilic properties. Besides, SPR can be considered as a useful instrument for study of the interaction of hydrophilic drugs with SA.

Myricetin (Myc) is one of the most important flavonoids in diet due to its abundance in foods with the highest antioxidant activity. The antioxidant activity of Myc was studied in cell-free and cell-based systems to evaluate the ROS protection efficiency of Myc. The studies were based on the assessment of reducing power of Myc according to ferric ion reduction and intracellular ROS level measurement by assaying the cellular fluorescence intensity using dichlorodihydrofluorescein (DCF) probe as an indicator for ROS in cells. Moreover, the antitoxic capability of Myc was assessed using MTT method. Data indicated that intracellular ROS are highly toxic and applying low concentration of Myc not only inhibited cellular ROS production but also was accompanying with the protection of cells against the highly toxic and the lethal effects of peroxide compounds. Because of strong correlation between cellular ROS and their cell toxic properties, the higher antioxidant potency of Myc in cell medium resulted in effectively blocking intracellular ROS and protecting cell death. This property is achieved by the help of high polar solubility and cell membrane permeability of Myc.

The purpose was to design a new construction containing influenza virus (H1N1) M2e gene and HA2 gene by bioinformatics approach, cloning the construct in to Escherichia coli and produce M2e-HA2 peptide.
The procedure was done by virus cultivation in SPF eggs, hemagglutination assay (HA), RNA isolation, RT-PCR, primers designed (DNAMAN 4 and Oligo7), virtual fusion construction translation (ExPASy), N-Glycosylated sites prediction (Ensemblegly-Iowa), complete open reading frame (ORF), stop codon studied (NCBI ORF Finder), rare codon determination (GenScript), Solvent accessibility of epitopes (Swiss-PdbViewer), antigenic sites prediction (Protean), fusion PCR of M2e-HA2 gene, sequence analysis, nested PCR, gel electrophoresis, double digestion of pET22b() plasmid and the fusion construct, ligation of them, transformation of the ligated vector (pET22b-M2e-HA2) to E.coli (BL21), mass culture the cloned bacterium ,induction the expression by isopropyl-beta-D-thiogalactopyranoside (IPTG), sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), purification the fusion peptide by Ni-NTA column, western blot to verify the purification.
In this study we developed a new approach for fusion of Influenza virus M2e (96 nucleotides) and HA2 (663 nucleotides) genes based on fusion PCR strategy and produced a fused fragment with 793 nucleotides. The construct was successfully cloned and expressed.
This construct is a 261 amino acid chimeric fusion peptide with about 30 KD molecular weight. According on the latest information; this is the first case of expression and purification M2e-HA2 fusion chimeric peptide, which could be used for development of a recombinant M2e-HA2 fusion protein vaccine.

Inhibition of angiotensin converting enzyme (i.e inhibition of cleaving angiotensin I to the potent vasoconstrictor angiotensin II) leads to the treatment and reduce the risk of cardiovascular diseases. Peptides (synthetic - natural) with ACE inhibitory activity were studied continuously during the last decades and resulting data were applied by medicinal chemists to design and develop new drugs. Their structure and activity/property relationships were studied during these years and different QSAR models were developed which assisted researchers and manufactures to reduce the cost of experiments. Developed models were reviewed in the present paper according to the applied dataset, descriptors, feature selection methods, model development and validation methods. The selected descriptors for different datasets and models were compared and discussed according to the experimental findings.

Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA), raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting “A site” of 16S rRNA) to riboswitches via docking method. There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8) hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with “16S rRNA A site”. Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA “A site” suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.

Recently discovered Anabaena variabilis phenylalanine ammonia lyase (AvPAL) proved to be a good candidate for enzyme replacement therapy of phenylketonuria. Outstanding stability properties of a mutant version of this enzyme, produced already in our laboratory, have led us to the idea of culture conditions optimization for soluble expression of this therapeutically valuable enzyme in E. coli. In the present study, the gene encoding mutant version of AvPAL was cloned into the pET28a expression vector. Different concentrations of IPTG, induction period, growth temperature, shaking speed, as well as different types of culture media were examined with respect to the amount of recombinant protein produced and specific activity of the enzyme. Based upon our findings, maximum amount of active mutant enzyme was attained by addition of 0.5 mM IPTG at 150 rpm to the TB culture media. The yield of active enzyme at cluture tempreature of 25 °C and induction period of 18 hour was the highest. The results of this study indicated that the yield of mutant AvPAL production in E. coli can be affected mainly by culture temperature and inducer concentration.

Estrogen receptor-alpha (ERα) mediates estrogen action in regulation of different levels of the hypothalamic-pituitary-testis axis. It has a key role in spermatogenesis. Estrogen receptor alpha knock-out (ER koα) male mice were infertile and severe impairment in spermatogenesis and seminiferous tubules was observed. Recently, it has been reported that microRNA (miRNA) mir-100 and let-7b were predicted to target ERα gene. MiRNA are small, endogenous, single stranded RNA molecules that regulate gene expression and have been implicated in various disease states. It has been proved that some miRNAs expression is tissue- and disease-specific, giving potential for identifying miRNAs as a diagnostic tool. In this study, the change in the expression levels of mir-100, let-7b and ERα expression levels were evaluated in oligospermic infertile patients (n=43) compared to control fertile subjects (n=43). After washing and separating sperms, total RNA was isolated and then cDNA was synthesized. The expression levels of mir-100 and let-7b and ERα were evaluated by real time PCR. Mir-100, let-7b levels were significantly higher than those in control group (P=0.008 and P=0.009, respectively). We have found that, ERα level was significantly decreased in comparison with normal group (P< 0.0001). Changes in mir-100, let-7b and ERα expression levels in oligospermic patients may be associated with the susceptibility and progression of infertility. The results of this study indicate that miRNA can have a key role in spermatogenesis and might have a diagnostic and prognostic value in men infertility.